GEO DataSets

(Submitter supplied) With an experimental RNomics, we identified 194 novel ncRNAs in silkworm through four developmental stages (egg, larva, pupa and adult). Oligos of 132 ncRNAs were sucessfully designed, the expression of these ncRNAs were analyzed by dual-channel microarray, results showed that 36 ncRNAs had significantly differential expression during development.

Organism:

Bombyx mori

Type:

Non-coding RNA profiling by array

Platform:

GPL10677

3 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Bombyx mori

Type:

Non-coding RNA profiling by array

Platform:

GPL10677

5 Samples

Download data: TXT

(Submitter supplied) We have performed the first systematic identification and analysis of intermediate size ncRNAs (50-500 nt) in the silkworm genome. We identified 194 novel ncRNAs, the expression profiles of them during the transitions from the egg to the first instar larva and from the fifth instar larva to the pupa were anlyzed by dual-channel microarray. Results showed that 12 ncRNAs had significantly differential expression during the two developmental transitions.

Organism:

Bombyx mori

Type:

Non-coding RNA profiling by array

Platform:

GPL10677

2 Samples

Download data: TXT

(Submitter supplied) As important roles of small RNA pathways, AGO proteins mediate interaction of incorporated small RNAs with their targets. The resolution of AGO associated small RNAs showed a significant landscape of AGO proteins and their binding small RNAs. To characterize small RNAs that associated with BmAGO2 protein in Bombyx mori, the small RNA population associated with BmAGO2 in BmN cells was extracted from the AGO immunoprecipitated complex and the small RNAs between 17nt to 50nt separated by a polyacrylamide gel electrophoresis were subjected to library construction and deep sequencing.The high throughput sequencing yielded a total of 11691441 reads, representing 813,702 unique reads with a abundance from 5731905 to 1.

Organism:

Bombyx mori

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16216

1 Sample

Download data: FA, TXT

(Submitter supplied) In this study, we employed a special size fractionation and cDNA library construction method followed by 454 deep sequencing to systematically profile rice intermediate-size ncRNAs. Our analysis resulted in the identification of 1349 ncRNAs in total, including 754 novel ncRNAs of an unknown functional category. Chromosome distribution of all identified ncRNAs showed no strand bias, and displayed a pattern similar to that observed in protein-coding genes with few chromosome dependencies. more...

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15856

2 Samples

Download data: BED

(Submitter supplied) ncRNA expression, including snoRNAs, across 11 tissues using polyA-neutral amplification Non-coding RNAs (ncRNAs) are an essential class of molecular species that have been difficult to monitor on high throughput platforms due to frequent lack of polyadenylation. Using a polyadenylation-neutral amplification protocol and next-generation sequencing, we explore ncRNA expression in eleven human tissues. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9115

11 Samples

Download data

(Submitter supplied) Small nucleolar RNAs (snoRNA) function in guiding 2'-O-methylation and pseudouridylation of ribosomal RNAs. But we found that knock down of a C/D box snoRNA, Bm-15, can induce apoptosis of insect Spodoptera frugiperda Sf9 cells. For the genome sequence of Spodoptera frugiperda is incomplete, here with the de novo sequencing method, transcriptome of Spodoptera frugiperda cell line Sf9 were sequenced after being transfected with overexpression vector and repression probes of snoRNA Bm-15. more...

Organism:

Spodoptera frugiperda

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17152

3 Samples

Download data: FA, XLS

(Submitter supplied) Recent advances in genome-wide techniques allowed the identification of thousands of non-coding RNAs with various sizes in eukaryotes, some of which have further been shown to serve important functions in many biological processes. However, in model plant Arabidopsis, novel intermediate-sized ncRNAs (im-ncRNAs) (50~300nt) have very limited information. By using a modified isolation strategy combined with deep-sequencing technology, we identified 838 im-ncRNAs in Arabidopsis globally. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16611

1 Sample

Download data: TXT